Depictions of youth sexuality are tricky. Shinji is supposed to be the character the audience identifies with and he’d be as horny and confused as anyone else his age. Shinji recognizing himself as a sexual being and seeing others as sexual beings is traumatic and that’s juxtaposed with the more traumatic realization that the fate of the world is in his hands. He’s between the latent and genital stages of psychosexual development. We see a lot of the world through Shinji’s eyes and that means we see how he sees the girls and women in the world. It’s an explicit adoption of an early teen male gaze. This causes a problem because accurately reproducing that gaze requires sexualizing children. I think the show could have depicted Shinji’s psychosexual development without adopting his gaze and been just as good but I can see where the writers were coming from.